If you want manual control on the creation of the transport order you can set the option in the ShipIT Setup Card to unposted documents . Now you have the availability of the ShipIT Quantity fields in the sales line.
On the Order Card, make sure you have at least one line with a ShipIT Quantity To Send larger than 0.
Release the order and click on the Create Transport Order action.
After creating the Transport Order, click Yes to open the Transport Order Card.
When working with Unposted documents the preferred way is to first book the transportorder and then post the warehouse/sales shipment. With this sequence you are able to store the transport order data in your shipments.